A fifth generation Lin Kuei warrior, Sub-Zero is the younger brother of the original Sub-Zero. When his brother failed to return from the Shaolin martial arts tournament, Sub-Zero took up his brother's mantle. He was assigned to complete the task his brother had failed in, the assassination of Shang Tsung. In order to do this, he entered the tournament hosted by Shao Kahn in the Outworld. Journeying to the Outworld, he vowed to avenge his death and defeat whoever was responsible. He performed admirably in the tournament, defeating many but killing no one. From some of the combatants, he learned that the ninja Scorpion had held a vendetta against his brother. Scorpion was present at the tournament, but he never came after Sub-Zero, to the Lin Kuei warrior's bewilderment. In the end, a warrior named Liu Kang defeated Shao Kahn, and Sub-Zero escaped through a portal back to Earth.
Returning to Lin Kuei headquarters with his friend Smoke, Sub-Zero learned that much had happened in his absence. In preperation for a possible Outworld invasion, the Lin Kuei had begun to entech their ninjas. Two cyborgs, Cyrax and Sektor, had already been created, and Sub-Zero and Smoke were ordered to undergo the process. Sub-Zero was loyal to the clan, but he realized that this was wrong, and refused. He and Smoke were forced to flee, and although Smoke was captures Sub-Zero managed to escape. While he was on the run, the Outworld invasion finally came to pass, and the Earth was turned into a grotesque imitation of the desolate Outworld. Pursued as he was, Sub-Zero still did his part to defend the Earth. He found himself under attack by Cyrax and Smoke, who had been turned into a cyborg as well. He appealed to his friend's still human soul, and the two managed to overcome and reprogram Cyrax. With the help of Sub-Zero and Smoke, the Earth warriors emerged victorious over the Outworld invaders and returned the Earth to normal.
After Shao Kahn's defeat, the Lin Kuei disbanded and Sub-Zero disappeared into the shadows. Years later, the Earth was again threatened, this time by the falled Elder god Shinnok. Through knowledge passed on to him by his brother, Sub-Zero knew how to defeat Shinnok, and thus joined with a group of Earth warriors to oppose him. Sub-Zero once again met up with Scorpion, who was now serving Shinnok. Sub-Zero finally learned that Scorpion had vowed to protect him, and still refused to do him harm. Sub-Zero revealed that Quan Chi, Shinnok's sorceror, had been responsible for the deaths of Scorpion's clan, not the original Sub-Zero. Enraged, Scorpion turned against his master and killed Quan Chi. This unbalanced Shinnok's power and led to his defeat. Sub-Zero bid the dissapearing Scorpion farewell, and once again returned to the shadows to await the time when he was needed again.